Added unit test for peekJob.pl

modules/Bio/EnsEMBL/Hive/Scripts/PeekJob.pm

@@ -37,7 +37,7 @@ sub peek {
     $job->load_parameters;
 
     my $unsub_params = $job->{'_unsubstituted_param_hash'};
-    print Dumper $unsub_params;
+    print Data::Dumper->Dump( [ $unsub_params ], [ qw(*unsubstituted_param_hash) ] );
     
     # my @ordered_params = sort { lc($a) cmp lc($b) } keys %$unsub_params;
     # print "{\n";

modules/Bio/EnsEMBL/Hive/Utils/Test.pm

@@ -46,7 +46,7 @@ use Bio::EnsEMBL::Hive::Scripts::StandaloneJob;
 our @ISA         = qw(Exporter);
 our @EXPORT      = ();
 our %EXPORT_TAGS = ();
-our @EXPORT_OK   = qw( standaloneJob init_pipeline runWorker beekeeper generate_graph visualize_jobs db_cmd seed_pipeline get_test_urls get_test_url_or_die run_sql_on_db load_sql_in_db make_new_db_from_sqls make_hive_db safe_drop_database all_source_files);
+our @EXPORT_OK   = qw( standaloneJob init_pipeline runWorker beekeeper generate_graph visualize_jobs db_cmd seed_pipeline tweak_pipeline peekJob get_test_urls get_test_url_or_die run_sql_on_db load_sql_in_db make_new_db_from_sqls make_hive_db safe_drop_database all_source_files);
 
 our $VERSION = '0.00';
 
@@ -345,6 +345,24 @@ sub visualize_jobs {
     return _test_ehive_script('visualize_jobs', @_);
 }
 
+=head2 peekJob
+
+  Arg[1]      : String $url. The location of the database
+  Arg[2]      : Arrayref $args. Extra arguments given to peekJob.pl
+  Arg[3]      : String $test_name (optional). The name of the test
+  Example     : peekJob($url, [-job_id => 1], 'Check params for job 1');
+  Description : Very generic function to run peekJob.pl on the given database with the given arguments
+  Returntype  : None
+  Exceptions  : TAP-style
+  Caller      : general
+  Status      : Stable
+
+=cut
+
+sub peekJob {
+    return _test_ehive_script('peekJob', @_);
+}
+
 
 =head2 db_cmd
 

t/03.scripts/peekJob_output.t

+#!/usr/bin/env perl
+
+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016-2019] EMBL-European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+use strict;
+use warnings;
+
+use Test::More;
+use Data::Dumper;
+use Test::JSON;
+use JSON qw(decode_json);
+
+use Capture::Tiny ':all';
+use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline runWorker beekeeper get_test_url_or_die run_sql_on_db peekJob);
+
+
+# eHive needs this to initialize the pipeline (and run db_cmd.pl)
+$ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) ) );
+
+my $pipeline_url = get_test_url_or_die();
+
+# Starting a first set of checks with a "GCPct" pipeline
+
+init_pipeline('Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::FailureTest_conf', $pipeline_url);
+
+my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeline_url );
+
+my $stdout = capture_stdout {
+    peekJob($pipeline_url, ["-job_id" => 1]);
+};
+$stdout =~ s/\s+//g;
+my $exp_stdout = "%unsubstituted_param_hash=('column_names'=>['value'],'inputlist'=>'#expr([0..#job_count#-1])expr#','job_count'=>10);";
+is( $stdout, $exp_stdout, 'Correct params reported' );
+
+done_testing();